Bayern Munich were never in danger of being toppled in the Champions League but the north London club gave them a few scares and will be in good heart for battles on the domestic front• Read Daniel Taylor's match report here

Back in the early days, when Mike Tyson would wear black shorts and black boots and fight in places like Albany and Glen Falls, his opponents would look beaten before the first bell. Never mind that Tyson was technically superior in all areas, the fear factor made the result a foregone conclusion. It was etched into every pore of the men who were pressed in front of him.

Bundesliga observers have come to consider Bayern Munich matches in much the same way. The reigning German, European and World champions have come to intimidate their domestic rivals to such an extent that some of them have virtually come to wonder why they bother.

Within the glut of pro-Bayern statistics, one stands out. Apart from the German Super Cup defeat by Borussia Dortmund in July, in effectively a glorified friendly, on similar lines to England's Community Shield, Bayern have not lost to a domestic opponent since October 2012.

Arsenal are a weightier proposition and the biggest positive that they took from their latest Champions League last-16 exit was that they did not flinch or stop fighting. They stayed tight during the first-half and, even at 3-0 down on aggregate, they found a response through Lukas Podolski.

Their chins remained up and it was, in many respects, a decent away performance. Arsène Wenger spoke of his players' pride and tremendous spirit.

But there was also the sense that Arsenal's approach was intrinsically limited; that the plan to hang in there and hang on, with the hope of landing a counter or two at some point was never really likely to topple the overwhelming favourite. Yet what else could they do? This is Bayern.

The hope has to be that the positives gleaned, chief among them the performances of the central defenders Laurent Koscielny and Per Mertesacker, below, together with that of Alex Oxlade-Chamberlain in midfield, can serve to fire them for the more realistic challenges ahead. There remains plenty to play for, not least the FA Cup. Win that and finish well in the Premier League and the season is a success. Anything less might not be so clever.

Arsenal had entered the Allianz Arena with the rare distinction of having beaten Bayern in recent times. Only themselves and Manchester City have managed to do so in almost 18 months (Dortmund's Super Cup win not withstanding), although on both occasions, the loss did not hurt Bayern. They advanced as the group winners earlier in the season despite losing here to City.

The evening had not started promisingly for Arsenal, when Wenger could only name six substitutes. With Yaya Sanogo and Nicklas Bendtner having succumbed to toe and knee injuries in the final training session before the squad departed on Monday, Wenger had taken Ryo Miyaichi as the 18th man. He never takes 19 players on European away trips.

But in a tragi-comic twist, Uefa would inform Arsenal that Miyaichi was not eligible for Champions League selection, having failed to meet the criteria for the squad's B list and been left off the A list. There was the feeling that it was only Miyaichi and he would surely not have featured anyway. On the upside, thank goodness it was noticed. Were the Japanese to have appeared, the consequences for Arsenal might have been grave.

Nonetheless, as Bayern named Toni Kroos and Thomas Müller among their substitutes, it was easy to imagine the Germans having a laugh at the expense of the English – again. First, there was Manuel Pellegrini's mathematical blunder when he failed to realise that another goal for City would have tipped the group in their favour and now this. Miyaichi watched from the stands.

If the first leg was coloured by Arsenal's explosive start, the tempo here was more measured and it was Bayern who dictated, hogging 64% of possession and probing for the opening. Arsenal did not necessarily need an early goal, rather the first goal and they were happy enough to shadow-box for as long as possible. Their priority was to stay in the contest.

Although Arjen Robben (his dive apart) and Franck Ribéry looked dangerous and Bayern repeatedly threatened to get in behind the Arsenal full-backs, Lukasz Fabianski was not overworked. His moment of glory was the injury-time penalty save from Müller.

It was a surprise to see Wenger start with Mesut Özil on the right, where he was always going to be asked to pitch into the defensive effort. He failed to track David Alaba and Ribéry on several occasions, which was the cause for much hand-wringing. Perhaps he was hamstrung by his hamstring, which Wenger said was cause for serious concern. Özil was withdrawn at half-time.

Wenger's formation could be described as 4-5-1 but Oxlade-Chamberlain did break out to provide encouragement from his central role. Preferred to Mathieu Flamini, there was assurance about his touch while he was crudely up-ended on more than one occasion. He contributed most wholeheartedly to the worries that Bayern had.

Arsenal's showed their character after the concession to Bastian Schweinsteiger with Podolski's goal and if it was a beautiful moment for him against his former club, it was a horrible one for the Norwegian referee Svein Oddvar Moen, who failed to spot the striker's push on Philipp Lahm. Podolski practically stopped in anticipation of the whistle and even Wenger said it was a foul.

Briefly, Arsenal threatened to cast off the shackles and they did cause moments of alarm. Bayern, however, were in charge.